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Yorodumi- PDB-8wl7: X-ray structure of Enterobacter cloacae allose-binding protein in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wl7 | ||||||
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Title | X-ray structure of Enterobacter cloacae allose-binding protein in complex with D-allose | ||||||
Components | Allose ABC transporter | ||||||
Keywords | SUGAR BINDING PROTEIN / Allose-binding protein | ||||||
Function / homology | Periplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / outer membrane-bounded periplasmic space / beta-D-allopyranose / Allose ABC transporter Function and homology information | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Kamitori, S. | ||||||
Funding support | 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: X-ray structures of Enterobacter cloacae allose-binding protein in complexes with monosaccharides demonstrate its unique recognition mechanism for high affinity to allose. Authors: Kamitori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wl7.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wl7.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 8wl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/8wl7 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/8wl7 | HTTPS FTP |
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-Related structure data
Related structure data | 8wl5C 8wl9C 8wlbC 1rpjS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32821.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: AI2656V1_0345, AI2799V1_0351, CGS27_05760 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G3F0C7 |
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#2: Sugar | ChemComp-ALL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10 mM D-allose, 200 mM ammonium sulfate, 25% (w/v) polyethylene glycol 3,350, 100 mM Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→48.94 Å / Num. obs: 35484 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.74→1.79 Å / Num. unique obs: 2590 / CC1/2: 0.757 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RPJ Resolution: 1.74→48.94 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.183 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.504 Å2
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Refinement step | Cycle: 1 / Resolution: 1.74→48.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Total num. of bins used: 20
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